[gmx-users] Re: Setting up a complex membrane simulation

Justin Lemkul jalemkul at vt.edu
Mon Nov 12 15:37:26 CET 2012

On 11/12/12 7:03 AM, jonas87 wrote:
> Ok, what i've currently done:
> I start with a pdb file of a single molecule Lipid_A and its topology and
> put it in a box:
> editconf -f Lipid_A.pdb -o Lipid_A-box.gro -bt triclinic -d 1.0
> I want a total of 128 molecules of this lipid in my system so I use genbox
> to add 127 more:
> genbox -cp Lipid_A-box.gro -ci Lipid_A.pdb -p Lipid_A.top -o 128_Lipid_A.pdb
> -nmol 127
> This only ads 8 molecules, I'm going to guess because more don't fit in my
> box. How do I deal with this? How can i know in advance how big i have to
> make the box?

You would need to know the volume of an individual lipid in the configuration 
that you are supplying, plus a volume that will allow for any other species in 
the system (like water) to yield the desired composition of the system.  The 
above series of commands yields a very small box, as you have found.  Most 
128-lipid membranes are on the order of 6-8 nm cubes, depending on the specific 
properties of the lipids being studied.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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